WO2013130381A1 - Cx3cr1-binding polypeptides - Google Patents

Cx3cr1-binding polypeptides Download PDF

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Publication number
WO2013130381A1
WO2013130381A1 PCT/US2013/027580 US2013027580W WO2013130381A1 WO 2013130381 A1 WO2013130381 A1 WO 2013130381A1 US 2013027580 W US2013027580 W US 2013027580W WO 2013130381 A1 WO2013130381 A1 WO 2013130381A1
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WIPO (PCT)
Prior art keywords
seq
cx3cr1
polypeptide
amino acid
polypeptide according
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PCT/US2013/027580
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English (en)
French (fr)
Inventor
Sanjaya Singh
Alisa K. WATERMAN
Erik Depla
Toon Laeremans
Diane Van Hoorick
Cedric Jozef Néotère VERVERKEN
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Boehringer Ingelheim International Gmbh
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First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=47884535&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2013130381(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to IN5756DEN2014 priority Critical patent/IN2014DN05756A/en
Priority to SG11201405283SA priority patent/SG11201405283SA/en
Priority to JP2014558920A priority patent/JP6101715B2/ja
Priority to CN201810147778.3A priority patent/CN108610421B/zh
Priority to KR1020147023938A priority patent/KR102008136B1/ko
Priority to CA2862182A priority patent/CA2862182A1/en
Priority to EA201400964A priority patent/EA028183B1/ru
Priority to MDA20140104A priority patent/MD4548C1/ro
Priority to UAA201410430A priority patent/UA115781C2/uk
Priority to MX2014009864A priority patent/MX349192B/es
Priority to CN201380016996.9A priority patent/CN104245735B/zh
Application filed by Boehringer Ingelheim International Gmbh filed Critical Boehringer Ingelheim International Gmbh
Priority to NZ627260A priority patent/NZ627260A/en
Priority to IL311502A priority patent/IL311502A/en
Priority to IL291571A priority patent/IL291571B1/en
Priority to AP2014007791A priority patent/AP2014007791A0/xx
Priority to CN202210946091.2A priority patent/CN115925938A/zh
Priority to BR112014021080-2A priority patent/BR112014021080B1/pt
Priority to AU2013226340A priority patent/AU2013226340B2/en
Priority to EP22168124.0A priority patent/EP4050027A3/en
Priority to EP13709641.8A priority patent/EP2820046B1/en
Publication of WO2013130381A1 publication Critical patent/WO2013130381A1/en
Priority to IL234018A priority patent/IL234018B2/en
Priority to PH12014501912A priority patent/PH12014501912A1/en
Priority to TNP2014000360A priority patent/TN2014000360A1/fr
Priority to HK15105855.6A priority patent/HK1205154A1/xx

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Definitions

  • the present invention relates to CX3CR1 -binding polypeptides, in particular polypeptides comprising specific immunoglobulin domains.
  • the invention also relates to nucleic acids encoding such polypeptides; to methods for preparing such polypeptides; to host cells expressing or capable of expressing such polypeptides; to compositions comprising such polypeptides; and to uses of such polypeptides or such compositions, in particular for prophylactic, therapeutic and diagnostic purposes.
  • CX3CR1 is a G-protein coupled integral membrane protein, which is a chemokine receptor. It is predominantly expressed on cell types such as monocytes, dendritic cells and T cells that have been associated with the initiation and progression of atherosclerotic plaques. It is upregulated on monocytes by oxidized lipids and mediates migration of these cells into and survival within plaques. Its unique ligand fractalkine (FKN) is expressed on the surface of vascular endothelial and smooth muscle cells in lesions where it modulates leukocyte adhesion. Fractalkine is also released into the circulation by proteolytic cleavage where it functions as a chemotactic agent.
  • FKN unique ligand fractalkine
  • CX3CR1 variant (V249I/T280M) with decreased activity has been shown to be associated with a lower risk of cardiovascular disease (coronary heart disease, cerebrovascular disease or peripheral vascular disease).
  • CX3CR1 co-localized with fractalkine which showed enhanced immunostaining by polyclonal antibodies within atherosclerotic plaques (Wong, 2002 Cardiovasc. Path. 1 1 :332). No fractalkine staining was observed in non-plaque arterial regions.
  • CX3CR1 is involved in cardiovascular diseases and the modulation of its activity could provide promising therapies.
  • antagonist molecules against CX3CR1 with beneficial pharmacological properties which can be used as therapeutic agents to treat diseases, in particular cardiovascular diseases in humans.
  • one aim of the present invention is to provide anti-CX3CR1 antagonist molecules, in particular anti-CX3CR1 antagonist molecules, which have high binding affinity to CX3CR1 .
  • a further aim of the present invention is to provide anti-CX3CR1 antagonist molecules, which have high specificity for CX3CR1 .
  • a further aim of the present invention is to provide anti-CX3CR1 antagonists, which have potent activity.
  • a further aim of the present invention is to provide anti-CX3CR1 antagonists, which have a favorable bioavailability and half-life.
  • a further aim of the present invention is to provide anti-CX3CR1 antagonists, which have favorable biophysical properties.
  • aims of the present invention include combinations of any of the aims set forth above.
  • the invention provides polypeptides which bind to human CX3CR1 and are capable of blocking the binding of human fractalkine to human CX3CR1 .
  • the polypeptide is an immunoglobulin comprising an antigen-binding domain comprising three complementarity determining regions CDR1 , CDR2 and CDR3, wherein said immunoglobulin binds to human CX3CR1 and is capable of blocking the binding of human fractalkine to human CX3CR1 .
  • the polypeptide comprises one or more anti-CX3CR1 immunoglobulin single variable domain, wherein said polypeptide is capable of blocking the binding of human fractalkine to human CX3CR1 .
  • polypeptide of the present invention is characterized by one or more of the following properties:
  • a polypeptide of the present invention comprises an anti- CX3CR1 immunoglobulin single variable domain and further comprises a half-life extending moiety, for example an albumin binding moiety, a polyethylene glycol molecule or a Fc domain.
  • a polypeptide of the present invention comprises two or more anti-CX3CR1 immunoglobulin single variable domains.
  • the two anti-CX3CR1 immunoglobulin single variable domains are covalently linked by a linker peptide.
  • the two anti- CX3CR1 immunoglobulin single variable domains in a polypeptide of the present invention have the same amino acid sequence.
  • the two anti- CX3CR1 immunoglobulin single variable domains in a polypeptide of the present invention have different amino acid sequences.
  • a polypeptide of the present invention comprises two anti-CX3CR1 immunoglobulin single variable domains and further comprises a half-life extending moiety, for example an albumin binding moiety, a polyethylene glycol molecule or a Fc domain.
  • a polypeptide of the present invention comprises a first anti- CX3CR1 immunoglobulin single variable domain covalently linked to an albumin binding moiety by a first linker peptide, wherein said albumin binding moiety is further covalently linked to a second anti-CX3CR1 immunoglobulin single variable domain by a second linker peptide.
  • a polypeptide of the present invention comprises an anti-CX3CR1 immunoglobulin single variable domain covalently linked to a Fc domain by a linker peptide.
  • such polypeptide comprising an anti-CX3CR1 immunoglobulin single variable domain covalently linked to a Fc domain by a linker peptide is provided as a dimer, for example through disulfide bridges.
  • the polypeptides of the present invention are used for the prevention, treatment, alleviation and/or diagnosis of CX3CR1 -associated diseases, disorders or conditions, in particular cardiovascular diseases, such as atherosclerosis.
  • the present invention provides:
  • Embodiment 1 An immunoglobulin comprising an antigen-binding domain comprising three complementarity determining regions CDR1 , CDR2 and CDR3, wherein said immunoglobulin binds to human CX3CR1 and is capable of blocking the binding of human fractalkine to human CX3CR1 .
  • Embodiment 2 A polypeptide comprising one or more anti-CX3CR1
  • immunoglobulin single variable domain wherein said polypeptide is capable of blocking the binding of human fractalkine to human CX3CR1 .
  • Embodiment 3 A polypeptide according to embodiment 2, wherein said anti- CX3CR1 immunoglobulin single variable domain consists essentially of four framework regions (FR1 , FR2, FR3 and FR4) and three complementary determining regions (CDR1 , CDR2 and CDR3).
  • Embodiment 4 A polypeptide according to embodiment 3, wherein said anti- CX3CR1 immunoglobulin single variable domain has the structure FR1 - CDR1 - FR2 - CDR2 - FR3 - CDR3 - FR4.
  • Embodiment 5 A polypeptide according to any one of embodiments 2 to 4, wherein said anti-CX3CR1 immunoglobulin single variable domain is an antibody domain.
  • Embodiment 6 A polypeptide according to embodiment 5, wherein said anti- CX3CR1 immunoglobulin single variable domain is a VH, VL, VHH, camelized VH, or VHH that is optimized for stability, potency, manufacturability and/or similarity to human framework regions.
  • Embodiment 7 A polypeptide according to any one of embodiments 1 to 6, wherein said polypeptide has an affinity to human CX3CR1 at:
  • Embodiment 8 A polypeptide according to any one of embodiments 1 to 7, wherein said polypeptide blocks the binding of human fractalkine to human CX3CR1 at an IC50 of less than or equal to 300nM, or less than or equal to " ⁇ ⁇ , or less than or equal to 20nM, or less than or equal to 10nM, or less than or equal to 5nM, or less than or equal to 2.5nM or less than or equal to 1 nM.
  • Embodiment 9 A polypeptide according to any one of embodiments 1 to 8, wherein said polypeptide inhibits fractalkine induced chemotaxis mediated by human CX3CR1 at an IC 5 o of less than or equal to 500 nM, or of less than or equal to 100 nM, or of less than or equal to 75 nM, or of less than or equal to 50 nM, or less than or equal to 1 0 nM or less than or equal to 5nM.
  • Embodiment 10 A polypeptide according to any one of embodiments 1 to 9, wherein said polypeptide inhibits fractalkine internalization mediated by human CX3CR1 at an IC 5 o of less than or equal to 10 nM, or less than or equal to 5nM or or less than or equal to 1 nM.
  • Embodiment 1 1 A polypeptide according to any one of embodiments 3 to 10, wherein said CDR3 has the amino acid sequence of Asp-Xaa1 -Arg-Arg-Gly-Trp- Xaa2-Xaa3-Xaa4-Xaa5 (SEQ ID NO: 197), wherein:
  • - Xaa1 is Pro, Ala or Gly;
  • - Xaa2 is Asp or Asn
  • - Xaa3 is Thr or Ser
  • - Xaa4 is Arg, Lys, Ala or Gly
  • - Xaa5 is Tyr or Phe.
  • Embodiment 12 A polypeptide according to any one of embodiments 3 to 1 1 , wherein:
  • - Xaa1 is Pro, Ala or Gly;
  • - Xaa2 is Asp or Asn
  • - Xaa4 is Arg or Lys
  • Embodiment 13 A polypeptide according to any one of embodiments 3 to 12, wherein said CDR3 has the amino acid sequence of Asp-Pro-Arg-Arg-Gly-Trp- Asp-Thr-Arg-Tyr (SEQ ID NO: 186).
  • Embodiment 14 A polypeptide according to any one of embodiments 3 to 10, wherein:
  • a) has the amino acid sequence of SEQ ID NO: 141 ;
  • b) has an amino acid sequence that has at least 80% amino acid identity with the amino acid sequence of SEQ ID NO: 141 ;
  • c) has an amino acid sequence that has 2, or 1 amino acid(s) difference with the amino acid sequence of SEQ ID NO: 141 , wherein
  • d) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a) has the amino acid sequence of SEQ ID NO: 164;
  • b) has an amino acid sequence that has at least 70% amino acid identity with the amino acid sequence of SEQ ID NO: 164;
  • c) has an amino acid sequence that has 4, 3, 2, or 1 amino acid(s)
  • d) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a) has the amino acid sequence of SEQ ID NO: 186;
  • b) has an amino acid sequence that has at least 70% amino acid identity the amino acid sequence of SEQ ID NO: 186;
  • c) has an amino acid sequence that has 3, 2, or 1 amino acid(s) difference with the amino acid sequences of SEQ ID NO: 186, wherein
  • d) has an amino acid sequence selected from any one of SEQ ID NO's:
  • Embodiment 15 A polypeptide according to any one of embodiments 3 to 10, wherein
  • said CDR1 has the amino acid sequence of SEQ ID NO: 146; ii) said CDR2 has an amino acid sequence that a) has at least 90% amino acid identity with the amino acid sequence of SEQ ID NO: 176 or b) has the amino acid sequence of SEQ ID NO: 176 or 177; and
  • said CDR3 has the amino acid sequence of SEQ ID NO: 191 .
  • Embodiment 16 A polypeptide according to any one of embodiments 3 to 10, wherein
  • a) has the amino acid sequence of SEQ ID NO: 147; or
  • b) has an amino acid sequence that has 6, 5, 4, 3, 2, or 1 amino acid(s) difference with the amino acid sequence of SEQ ID NO: 147, wherein
  • a) has the amino acid sequence of SEQ ID NO: 179; or
  • b) has an amino acid sequences that has 4, 3, 2, or 1 amino acid(s) difference with the amino acid sequence of SEQ ID NO: 179, wherein
  • c) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a) has the amino acid sequence of SEQ ID NO: 192; or has an amino acid sequence that has at least 80% amino acid identity with the amino acid sequence of SEQ ID NO: 192; or
  • Embodiment 17 A polypeptide according to embodiment 3, wherein the amino acid sequences of said CDR1 , CDR2 and CDR3 are set forth in:
  • Embodiment 18 A polypeptide according to embodiment 3, wherein the amino acid sequences of said CDR1 , CDR2 and CDR3 are set forth in:
  • Embodiment 19 A polypeptide according to embodiment 3, wherein the amino acid sequences of said CDR1 , CDR2 and CDR3 are set forth in:
  • Embodiment 20 A polypeptide according to embodiment 3, wherein the amino acid sequences of said CDR1 , CDR2 and CDR3 are set forth in: SEQ ID NO's: 141 , 1 64 and 1 86, respectively, or SEQ ID NO's: 141 , 162 and 1 86, respectively
  • Embodiment 21 A polypeptide according to embodiment 3, wherein the amino acid sequences of said CDR1 , CDR2 and CDR3 are set forth in: SEQ ID NO's: 213, 214 and 1 86 respectively, SEQ ID NO's: 21 3, 221 and 186 respectively, or SEQ ID NO's: 141 , 162 and 186 respectively.
  • Embodiment 22 A polypeptide according to any one of embodiments 2 to 10, wherein said anti-CX3CR1 immunoglobulin single variable domain is a VHH domain comprising the sequence set forth in:
  • amino acid sequences that have at least 90% amino acid identity with the amino acid sequences of SEQ ID NO: 3;
  • amino acid sequences that have 1 1 , 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid difference with the amino acid sequences of SEQ ID NO: 3; or d) an amino acid sequence of any one of SEQ ID NO: 1 -48, 1 21 -140 or 222- 224.
  • Embodiment 23 A polypeptide according to any one of embodiments 2 to 10, wherein said anti-CX3CR1 immunoglobulin single variable domain is a VHH domain comprising the sequence set forth in:
  • amino acid sequences of SEQ ID NO: 49 b) an amino acid sequence that has at least 95% amino acid identity with the amino acid sequences of SEQ ID NO: 49; c) an amino acid sequence that has 5, 4, 3, 2, or 1 amino acid difference with the amino acid sequences of SEQ ID NO: 49; or
  • Embodiment 24 A polypeptide according to any one of embodiments 2 to 10, wherein said anti-CX3CR1 immunoglobulin single variable domain is a VHH domain comprising the sequence set forth in:
  • Embodiment 25 A polypeptide according to embodiment 2, wherein said anti- CX3CR1 immunoglobulin single variable domain comprises the sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 3.
  • Embodiment 26 A polypeptide according to embodiment 2, wherein said anti- CX3CR1 immunoglobulin single variable domain comprises the sequence set forth in any one of SEQ ID NO: 121 -140 or SEQ ID NO: 222-224.
  • Embodiment 27 A polypeptide according to any of one of the embodiments above, which is humanized and/or optimized for stability, potency,
  • Embodiment 28 A polypeptide according to embodiment 27, which is humanized and/or sequence optimized in one or more of the following positions (according to Kabat numbering): 1 , 1 1 , 14, 16, 74, 83, 108.
  • Embodiment 29 A polypeptide according to embodiment 28, comprising one or more of the following mutations: E1 D, S1 1 L, A14P, E16G, A74S, K83R, Q108L.
  • Embodiment 30 A polypeptide according to any one of embodiments 3-29, in which:
  • FR1 is selected from SEQ ID NO's: 198-204;
  • FR2 is selected from SEQ ID NO's: 205-208;
  • FR3 is selected form SEQ ID NO's: 209-210; and/or
  • FR4 is selected from SEQ ID NO's: 21 1 -212.
  • Embodiment 31 A polypeptide according to any one of embodiments 3-30, which is humanized and/or sequence optimized in one or more of the following positions (according to Kabat numbering): 52, 53.
  • Embodiment 32 A polypeptide according to embodiment 31 , comprising one or more of the following mutations: N52S, S53T.
  • Embodiment 33 A polypeptide according to any one of embodiments 3-32, in which CDR2 is selected from SEQ ID NO's: 214-221 .
  • Embodiment 34 A polypeptide according to any one of embodiments 2-33, wherein said anti-CX3CR1 immunoglobulin single variable domain comprises the sequence set forth in any of SEQ ID NO's: 138-140 or 222-224.
  • Embodiment 35 A polypetide according to any one of embodiments 22 to 26, wherein said VHH domain consists of any one of said amino acid sequences.
  • Embodiment 36 A polypeptide according to any one of embodiments 2 to 35, wherein said immunoglobulin single variable domain cross-blocks the binding of at least one of the immunoglobulin single variable domains of SEQ ID NO's: 1 - 120, 1 21 -140 and 222-224 to CX3CR1 .
  • Embodiment 37 A polypeptide according to any one of embodiments 2 to 35, wherein said immunoglobulin single variable domain is cross-blocked from binding to CX3CR1 by at least one of the amino acid sequences of SEQ ID NO's: 1 -120, 1 21 -140 and 222-224.
  • Embodiment 38 A polypeptide according to any one of embodiments 2 to 37, wherein the polypeptide further comprises a half-life extending moiety.
  • Embodiment 39 A polypeptide according to embodiment 38, wherein said half- life extending moiety is covalently linked to said polypeptide and is selected from the group consisting of an albumin binding moiety, such as an anti-albumin immunoglobulin domain, a transferrin binding moiety, such as an anti-transferrin immunoglobulin domain, a polyethylene glycol molecule, a recombinant polyethylene glycol molecule, human serum albumin, a fragment of human serum albumin, an albumin binding peptide or a Fc domain.
  • an albumin binding moiety such as an anti-albumin immunoglobulin domain
  • a transferrin binding moiety such as an anti-transferrin immunoglobulin domain
  • Embodiment 40 A polypeptide according to embodiment 38 or 39, wherein said half-life extending moiety consists of an anti-albumin immunoglobulin single variable domain.
  • Embodiment 41 A polypeptide according to embodiment 40, wherein the immunoglobulin single variable domain is selected from a VHH domain, a humanized VHH domain, a camelized VH domain, a domain antibody, a single domain antibody and/or "dAb"s.
  • Embodiment 42 A polypeptide according to embodiment 41 , wherein the anti- albumin immunoglobulin single variable domain is selected from SEQ ID NO's: 230-232.
  • Embodiment 43 A polypeptide according to any one of embodiment 2 to 39, wherein said polypeptide is linked to an Fc portion (such as a human Fc, for example as set forth in SEQ ID NO: 252), optionally via a suitable linker or hinge region.
  • Fc portion such as a human Fc, for example as set forth in SEQ ID NO: 252
  • Embodiment 44 A polypeptide according to any one of embodiments 2 to 39, wherein said polypeptide is further linked to one or more constant domains (for example, 2 or 3 constant domains that can be used as part of/to form an Fc portion), to an Fc portion and/or to one or more antibody parts, fragments or domains that confer one or more effector functions to the polypeptide of the invention and/or may confer the ability to bind to one or more Fc receptors, optionally via a suitable linker or hinge region.
  • constant domains for example, 2 or 3 constant domains that can be used as part of/to form an Fc portion
  • Embodiment 45 A polypeptide according to any one of embodiments 2 to 37, wherein said polypeptide further comprises a second immunoglobulin single variable domain, preferably a second anti-CX3CR1 immunoglobulin single variable domain.
  • Embodiment 46 A polypeptide according to embodiment 45, wherein said first and said second immunoglobulin single variable domains are covalently linked by a linker peptide.
  • Embodiment 47 A polypeptide according to embodiment 45 or 46, wherein said second immunoglobulin single variable domains essentially consist of four framework regions (FR1 to FR4) and three complementary determining regions (CDR1 to CDR3).
  • Embodiment 48 A polypeptide according to any one of embodiments 45 to 47, wherein said first and said second immunoglobulin single variable domains are antibody domains.
  • Embodiment 49 A polypeptide according to any one of embodiments 45 to 48, wherein said first and second immunoglobulin single variable domains are a VH, VL, VHH, camelized VH, or VHH that is optimized for stability, potency, manufacturability and/or similarity to human framework regions.
  • Embodiment 50 A polypeptide according to any one of embodiments 45 to 49, wherein said CDR1 to CDR3 of said second immunoglobulin single variable domain are set forth in any one of embodiments 1 1 to 21 .
  • Embodiment 51 A polypeptide according to any one of embodiments 45 to 50, wherein said first and said second immunoglobulin single variable domains comprise the same CDR3.
  • Embodiment 52 A polypeptide according to embodiment 51 , wherein said CDR3 is set forth in any one of embodiment 1 1 to 13.
  • Embodiment 53 A polypeptide according to any one of embodiments 45 to 53, wherein said first and said second immunoglobulin single variable domains comprise the same CDR1 , CDR2 and CDR3.
  • Embodiment 54 A polypeptide according to embodiment 53, wherein said CDR1 to CDR3 are set forth in any one of embodiments 1 1 to 21 .
  • Embodiment 55 A polypeptide according to any one of embodiments 45 to 54, wherein said first and said second immunoglobulin single variable domains comprise the same VHH domain.
  • Embodiment 56 A The polypeptide according to any one of embodiments 45 to 55, wherein said VHH domain is set forth in any one of embodiments 22 to 37.
  • Embodiment 57 A polypeptide comprising a first immunoglobulin single variable domain comprising the CDR1 , CDR2 and CDR3 set forth SEQ ID NO's: 141 , 164 and 1 86 or SEQ ID NO's: 141 , 162 and 1 86 and a second immunoglobulin single variable domain as set forth in any one of embodiments 2 to 37.
  • Such a polypeptide may in particular be a polypeptide according to any of embodiments 45 to 56.
  • Embodiment 58 A polypeptide according to embodiment 57, wherein said first immunoglobulin single variable domain comprises the CDR1 , CDR2 and CDR3 set forth in SEQ ID NO's: 213, 214 and 186, SEQ ID NO's: 213, 221 and 186 or SEQ ID NO's: 141 , 162 and 186.
  • Embodiment 59 A polypeptide according to embodiment 57 or 58, wherein said second immunoglobulin single variable domain comprises the CDR1 , CDR2 and CDR3 set forth SEQ ID NO's: 141 , 164 and 186 or SEQ ID NO's: 141 , 1 62 and 186.
  • Embodiment 60 A polypeptide according to embodiment 57 Or 58, wherein said second immunoglobulin single variable domain comprises the CDR1 , CDR2 and CDR3 set forth in: SEQ ID NO's: 213, 214 and 186, SEQ ID NO's: 213, 221 and 186 or SEQ ID NO's: 141 , 162 and 186.
  • Embodiment 61 A polypeptide comprising a first immunoglobulin single variable domain, wherein said first immunoglobulin single variable domain is a VHH domain comprising the sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 3 and a second immunoglobulin single variable domain according to any one of embodiments 2 to 37.
  • Such a polypeptide may in particular be a polypeptide according to any of embodiments 45 to 60.
  • Embodiment 62 A polypeptide according to embodiment 61 , wherein said first immunoglobulin single variable domain is a VHH domain comprising the sequence set forth in any one of SEQ ID NO: 121 -140 or 222-224.
  • Embodiment 63 A polypeptide according to embodiment 61 or 62, wherein said second immunoglobulin single variable domain is a VHH domain comprising the sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 3.
  • Embodiment 64 A polypeptide according to embodiment 63, wherein said second immunoglobulin single variable domain is a VHH domain comprising the sequence set forth in any one of SEQ ID NO: 121 -140 or 222-224.
  • Embodiment 65 A polypeptide according to any one of embodiments 45 to 64, wherein the polypeptide further comprises a half-life extending moiety.
  • Embodiment 66 A polypeptide according to embodiment 65, wherein said half- life extending moiety is covalently linked to said polypeptide and is selected from the group consisting of an albumin binding moiety, such as an anti-albumin immunoglobulin domain, a transferrin binding moiety, such as an anti-transferrin immunoglobulin domain, a polyethylene glycol molecule, a recombinant polyethylene glycol molecule, human serum albumin, a fragment of human serum albumin, an albumin binding peptide or a Fc domain.
  • an albumin binding moiety such as an anti-albumin immunoglobulin domain
  • a transferrin binding moiety such as an anti-transferrin immunoglobulin domain
  • Embodiment 67 A polypeptide according to embodiment 66, wherein said half- life extending moiety consists of an anti-albumin immunoglobulin single variable domain.
  • Embodiment 68 A polypeptide according to embodiment 67, wherein the immunoglobulin single variable domain is selected from a VHH domain, a humanized VHH domain, a camelized VH domain, a domain antibody, a single domain antibody and/or "dAb"s.
  • Embodiment 69 A polypeptide according to embodiment 68, wherein the anti- albumin immunoglobulin single variable domain is selected from SEQ ID NO's: 230-232.
  • Embodiment 70 A polypeptide according to any one of embodiments 45 to 64, wherein said polypeptide is linked to an Fc portion (such as a human Fc, for example as set forth in SEQ ID NO: 252), optionally via a suitable linker or hinge region.
  • Fc portion such as a human Fc, for example as set forth in SEQ ID NO: 252
  • Embodiment 71 A polypeptide according to any one of embodiments 45 to 66, wherein said polypeptide is further linked to one or more constant domains (for example, 2 or 3 constant domains that can be used as part of/to form an Fc portion), to an Fc portion and/or to one or more antibody parts, fragments or domains that confer one or more effector functions to the polypeptide of the invention and/or may confer the ability to bind to one or more Fc receptors, optionally via a suitable linker or hinge region.
  • constant domains for example, 2 or 3 constant domains that can be used as part of/to form an Fc portion
  • Embodiment 72 A polypeptide comprising the amino acid sequence of any one of SEQ ID NO: 225-227.
  • Embodiment 73 A polypeptide comprising the amino acid sequence of any one of SEQ ID NO: 249 or 277-281 .
  • Embodiment 74 A polypeptide comprising the amino acid sequence of any one of SEQ ID NO: 257-262.
  • Embodiment 75 A polypeptide comprising the amino acid sequence of any one of SEQ ID NO: 253 or 254.
  • Embodiment 76 A polypeptide comprising the amino acid sequence of any one of SEQ ID NO: 263 or 266.
  • Embodiment 77 A polypeptide comprising the amino acid sequence of any one of SEQ ID NO: 267-276 and 282.
  • Embodiment 78 A nucleic acid molecule comprising a region encoding a polypeptide according to any one of embodiments 1 to 77.
  • Embodiment 79 An expression vector comprising a nucleic acid molecule according to embodiment 78.
  • Embodiment 80 A host cell carrying an expression vector comprising a nucleic acid molecule, said nucleic acid molecule comprising a region encoding a polypeptide according to any one of embodiments 1 to 77, wherein said host cell is capable of expressing a polypeptide according to any one of embodiments 1 to 77, and wherein said host cell is a prokaryotic or a eukaryotic cell.
  • Embodiment 81 A pharmaceutical composition comprising (i) as the active ingredient, one or more polypeptides according to any one of embodiments 1 to 77, and (ii) a pharmaceutically acceptable carrier, and optionally (iii) a diluent, excipient, adjuvant and/or stabilizer.
  • Embodiment 82 A method of manufacturing a polypeptide according to any one of embodiments 1 to 77, comprising the steps of
  • polypeptide according to any one of embodiments 1 to 77,
  • said host cell carrying an expression vector comprising a nucleic acid molecule, said nucleic acid molecule comprising a region encoding a polypeptide according to any one of embodiments 1 to 77, and wherein said host cell is a prokaryotic or a eukaryotic cell;
  • Embodiment 83 A method of using a polypeptide according to any one of embodiments 1 to 77 for the treatment, prevention or alleviation of a disease, disorder or condition, in particular in a human being.
  • Embodiment 84 The method of embodiment 83, wherein said disease, disorder or condition is a CX3CR1 -associated disease, disorder or condition.
  • Embodiment 85 The method of embodiment 83, wherein said disease, disorder or condition is atherosclerosis.
  • Embodiment 86 An injectable pharmaceutical composition comprising the polypeptide according to any one of embodiments 1 to 77, said composition being suitable for intravenous or subcutaneous injection in a human being.
  • Embodiment 87 A method for preventing and/or treating a disease or disorder that is associated with CX3CR1 , wherein said method comprises administering to a subject in need thereof a pharmaceutically active amount of at least one polypeptide according to any one of embodiments 1 to 77.
  • Embodiment 88 A method of embodiment 85, further comprising administering an additional therapeutic agent selected from the group consisting of a statin, an antiplatelet, an anticoagulant, an antidiabetic and an antihypertensive.
  • an additional therapeutic agent selected from the group consisting of a statin, an antiplatelet, an anticoagulant, an antidiabetic and an antihypertensive.
  • Embodiment 89 A method for inhibiting the binding of CX3CR1 to fractalkine in a mammalian cell, comprising administering to the cell a polypeptide according to any one of embodiments 1 to 77, whereby signaling mediated by the fractalkine is inhibited.
  • Embodiment 90 A method for detecting and/or quantifying CX3CR1 levels in a biological sample by contacting the sample with a polypeptide according to any one of embodiments 1 to 77 and detecting binding of the polypeptide with
  • Embodiment 91 A method for diagnosing an CX3CR1 -associated disorder or for determining if a subject has an increased risk of developing an CX3CR1 - associated disorder, wherein the method comprises contacting a biological sample from a subject with a polypeptide according to any one of embodiments 1 to 77 and detecting binding of the polypeptide to CX3CR1 to determine the expression or concentration of CX3CR1 .
  • Embodiment 92 A polypeptide according to any one of embodiments 1 to 77 for use in the treatment, prevention or alleviation of a disease, disorder or condition, in a human being.
  • Embodiment 93 The polypeptide for use according to embodiment 92, wherein the disease, disorder or condition is a CX3CR1 -associated disease, disorder or condition.
  • Embodiment 94 The polypeptide for use according to embodiment 92, wherein the disease, disorder or condition is selected from cardio- and cerebrovascular atherosclerotic disorders, peripheral artery disease, restenosis, diabetic nephropathy, glomerulomephritis, human crescentic glomerulonephritis, IgA nephropathy, membranous nephropathy, lupus nephritis, vasculitis including Henoch-Schonlein purpura and Wegener's granulomatosis, rheumatoid arthritis, osteoarthritis, allograft rejection, systemic sclerosis, neurodegenerative disorders and demyelinating disease, multiple sclerosis (MS), Alzheimer's disease, pulmonary diseases such as COPD, asthma,neuropathic pain, inflammatory pain, or cancer.
  • the disease, disorder or condition is selected from cardio- and cerebrovascular atherosclerotic disorders, peripheral artery disease, restenosis, diabetic nephropathy
  • Embodiment 95 The polypeptide for use according to embodiment 92, wherein the disease, disorder or condition is atherosclerosis.
  • Embodiment 96 Use of a polypeptide according to any of embodiments 1 to 77 for the manufacture of a medicament for the treatment, prevention or alleviation of a disease, disorder or condition, in a human being.
  • Embodiment 97 The method according to embodiment 87, wherein the disease or disorder is selected from cardio- and cerebrovascular atherosclerotic disorders, peripheral artery disease, restenosis, diabetic nephropathy, glomerulonephritis, human crescentic glomerulonephritis, IgA nephropathy, membranous nephropathy, lupus nephritis, vasculitis including Henoch-Schonlein purpura and Wegener's granulomatosis, rheumatoid arthritis, osteoarthritis, allograft rejection, systemic sclerosis, neurodegenerative disorders and demyelinating disease, multiple sclerosis (MS), Alzheimer's disease, pulmonary diseases such as COPD, asthma,neuropathic pain, inflammatory pain, or cancer.
  • the disease or disorder is selected from cardio- and cerebrovascular atherosclerotic disorders, peripheral artery disease, restenosis, diabetic nephropathy, glomerulonephriti
  • Embodiment 98 The method according to embodiment 87, wherein the disease, disorder or condition is atherosclerosis.
  • Embodiment 99 A diagnostic kit or diagnostic method comprising a polypeptide according to any one of embodiments 1 to 77, or the use thereof.
  • Embodiment 100 A diagnostic kit or diagnostic method according to embodiment 99, for the diagnosis of at least one of cardio- and cerebrovascular atherosclerotic disorders, peripheral artery disease, restenosis, diabetic nephropathy, glomerulomephritis, human crescentic glomerulonephritis, IgA nephropathy, membranous nephropathy, lupus nephritis, vasculitis including Henoch-Schonlein purpura and Wegener's granulomatosis, rheumatoid arthritis, osteoarthritis, allograft rejection, systemic sclerosis, neurodegenerative disorders and demyelinating disease, multiple sclerosis (MS), Alzheimer's disease, pulmonary diseases such as COPD, asthma,neuropathic pain, inflammatory pain, or cancer.
  • pulmonary diseases such as COPD, asthma,neuropathic pain, inflammatory pain, or cancer.
  • immunoglobulin and “immunoglobulin sequence” - whether used herein to refer to a heavy chain antibody or to a conventional 4-chain antibody - are used as general terms to include both the full- size antibody, the individual chains thereof, as well as all parts, domains or fragments thereof (including but not limited to antigen-binding domains or fragments such as VHH domains or VH/VL domains, respectively).
  • sequence as used herein (for example in terms like “immunoglobulin sequence”, “antibody sequence”, “(single) variable domain sequence", “VHH sequence” or “protein sequence”), should generally be understood to include both the relevant amino acid sequence as well as nucleic acid sequences or nucleotide sequences encoding the same, unless the context requires a more limited interpretation; c)
  • domain (of a polypeptide or protein) as used herein refers to a folded protein structure which has the ability to retain its tertiary structure independently of the rest of the protein.
  • immunoglobulin domain refers to a globular region of an antibody chain (such as e.g. a chain of a conventional 4-chain antibody or of a heavy chain antibody), or to a polypeptide that essentially consists of such a globular region.
  • Immunoglobulin domains are characterized in that they retain the immunoglobulin fold characteristic of antibody molecules, which consists of a 2-layer sandwich of about 7 antiparallel beta-strands arranged in two beta-sheets, optionally stabilized by a conserved disulphide bond.
  • immunoglobulin variable domain as used herein means an immunoglobulin domain essentially consisting of four "framework regions” which are referred to in the art and hereinbelow as “framework region 1 " or "FR1 "; as “framework region 2" or”FR2"; as “framework region 3" or "FR3”; and as
  • framework region 4" or "FR4" which framework regions are interrupted by three “complementarity determining regions” or “CDRs”, which are referred to in the art and hereinbelow as “complementarity determining region Tor “CDR1 "; as “complementarity determining region 2" or “CDR2”; and as “complementarity determining region 3” or “CDR3”, respectively.
  • CDR1 complementary determining region
  • CDR2 complementary determining region 2
  • CDR3 complementarity determining region 3
  • the general structure or sequence of an immunoglobulin variable domain can be indicated as follows: FR1 - CDR1 - FR2 - CDR2 - FR3 - CDR3 - FR4. It is the immunoglobulin variable domain(s) that confer specificity to an antibody for the antigen by carrying the antigen-binding site.
  • immunoglobulin single variable domain and “single variable domain” as used herein mean an immunoglobulin variable domain which is capable of specifically binding to an epitope of the antigen without pairing with an additional variable immunoglobulin domain.
  • immunoglobulin single variable domains in the meaning of the present invention are "domain antibodies”, such as the immunoglobulin single variable domains VH and VL (VH domains and VL domains).
  • immunoglobulin single variable domains are " VHH domains" (or simply "VHHs") from camelids, as defined hereinafter.
  • the antigen-binding domain of a conventional 4- chain antibody such as an IgG, IgM, IgA, IgD or IgE molecule; known in the art
  • a conventional 4- chain antibody such as an IgG, IgM, IgA, IgD or IgE molecule; known in the art
  • a Fab fragment, a F(ab')2 fragment, an Fv fragment such as a disulphide linked Fv or a scFv fragment, or a diabody (all known in the art) derived from such conventional 4-chain antibody would normally not be regarded as an immunoglobulin single variable domain, as, in these cases, binding to the respective epitope of an antigen would normally not occur by one (single) immunoglobulin domain but by a pair of (associating) immunoglobulin domains such as light and heavy chain variable domains, i.e.
  • VHH domains also known as VHHs, V H H domains, VHH antibody fragments, and VHH antibodies, have originally been described as the antigen binding immunoglobulin (variable) domain of "heavy chain antibodies” (i.e. of "antibodies devoid of light chains”; Hamers-Casterman C, Atarhouch T,
  • VHH domain has been chosen in order to distinguish these variable domains from the heavy chain variable domains that are present in conventional 4-chain antibodies (which are referred to herein as "V H domains” or “VH domains”) and from the light chain variable domains that are present in conventional 4-chain antibodies (which are referred to herein as "V L domains" or “VL domains").
  • VHH domains can specifically bind to an epitope without an additional antigen binding domain (as opposed to VH or VL domains in a conventional 4-chain antibody, in which case the epitope is recognized by a VL domain together with a VH domain).
  • VHH domains are small, robust and efficient antigen recognition units formed by a single immunoglobulin domain.
  • VHH domain VHH, V H H domain, VHH antibody fragment, VHH antibody, as well as "Nanobody®” and “Nanobody® domain”
  • “Nanobody” being a trademark of the company Ablynx N.V.; Ghent; Belgium
  • immunoglobulin single variable domains having the structure: FR1 -CDR1 -FR2- CDR2-FR3-CDR3-FR4 and specifically binding to an epitope without requiring the presence of a second immunoglobulin variable domain
  • hallmark residues as defined in e.g. WO2009/1 09635, Fig. 1 .
  • VHH domains are numbered according to the general numbering for V H domains given by Kabat et al. ("Sequence of proteins of immunological interest", US Public Health Services, NIH Bethesda, MD,
  • - FR1 comprises the amino acid residues at positions 1 -30,
  • - CDR1 comprises the amino acid residues at positions 31 -35
  • - FR2 comprises the amino acids at positions 36-49,
  • - CDR2 comprises the amino acid residues at positions 50-65
  • - FR3 comprises the amino acid residues at positions 66-94
  • - CDR3 comprises the amino acid residues at positions 95-102, and
  • - FR4 comprises the amino acid residues at positions 103-1 13.
  • the total number of amino acid residues in each of the CDRs may vary and may not correspond to the total number of amino acid residues indicated by the Kabat numbering (that is, one or more positions according to the Kabat numbering may not be occupied in the actual sequence, or the actual sequence may contain more amino acid residues than the number allowed for by the Kabat numbering).
  • the numbering according to Kabat may or may not correspond to the actual numbering of the amino acid residues in the actual sequence.
  • the total number of amino acid residues in a VHH domain will usually be in the range of from 1 10 to 1 20, often between 1 1 2 and 1 15. It should however be noted that smaller and longer sequences may also be suitable for the purposes described herein.
  • VHH domains (which have been "designed" by nature to functionally bind to an antigen without the presence of, and without any interaction with, a light chain variable domain) can function as a single, relatively small, functional antigen- binding structural unit, domain or polypeptide. This distinguishes the VHH domains from the VH and VL domains of conventional 4-chain antibodies, which by themselves are generally not suited for practical application as single antigen- binding proteins or immunoglobulin single variable domains, but need to be combined in some form or another to provide a functional antigen-binding unit (as in for example conventional antibody fragments such as Fab fragments; in scFv's, which consist of a VH domain covalently linked to a VL domain).
  • a functional antigen-binding unit as in for example conventional antibody fragments such as Fab fragments; in scFv's, which consist of a VH domain covalently linked to a VL domain.
  • VHH domains - either alone or as part of a larger polypeptide - offers a number of significant advantages over the use of conventional VH and VL domains, scFv's or conventional antibody fragments (such as Fab- or F(ab')2-fragments): - only a single domain is required to bind an antigen with high affinity and with high selectivity, so that there is no need to have two separate domains present, nor to assure that these two domains are present in the right spacial conformation and configuration (i.e. through the use of especially designed linkers, as with scFv's);
  • VHH domains can be expressed from a single gene and require no post- translational folding or modifications
  • VHH domains can easily be engineered into multivalent and multispecifi ' c formats (as further discussed herein);
  • VHH domains are highly soluble and do not have a tendency to aggregate (as with the mouse-derived antigen-binding domains described by Ward et al., Nature 341 : 544-546 (1989));
  • VHH domains are highly stable to heat, pH, proteases and other denaturing agents or conditions and, thus, may be prepared, stored or transported without the use of refrigeration equipments, conveying a cost, time and environmental savings;
  • VHH domains and polypeptides containing the same can be produced using microbial fermentation (e.g. as further described below) and do not require the use of mammalian expression systems, as with for example conventional antibody fragments;
  • VHH domains are relatively small (approximately 15 kDa, or 10 times smaller than a conventional IgG) compared to conventional 4-chain antibodies and antigen-binding fragments thereof, and therefore
  • VHH domains can show so-called cavity-binding properties (inter alia due to their extended CDR3 loop, compared to conventional VH domains) and can therefore also access targets and epitopes not accessible to conventional 4-chain antibodies and antigen-binding fragments thereof.
  • Methods of obtaining VHH domains binding to a specific antigen or epitope have been described earlier, e.g. in WO2006/040153 and WO2006/122786.
  • VHH domains derived from camelids can be
  • a humanized VHH domain can contain one or more fully human framework region sequences, and, in an even more specific embodiment, can contain human framework region sequences derived from DP-29, DP-47, DP-51 , or parts thereof, optionally combined with JH sequences, such as JH5.
  • Domain antibodies also known as “Dab”s, “Domain Antibodies”, and “dAbs” (the terms “Domain Antibodies” and “dAbs” being used as trademarks by the GlaxoSmithKline group of companies) have been described in e.g. Ward, E.S., et al. ⁇ "Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli"; Nature 341 : 544-546 (1989); Holt, L.J. et al. ⁇ "Domain antibodies: proteins for therapy”; TRENDS in Biotechnology 21 (1 1 ): 484-490 (2003); and WO2003/002609.
  • Domain antibodies essentially correspond to the VH or VL domains of non- camelid mammalians, in particular human 4-chain antibodies.
  • specific selection for such antigen binding properties is required, e.g. by using libraries of human single VH or VL domain sequences.
  • Domain antibodies have, like VHHs, a molecular weight of approximately 13 to approximately 16 kDa and, if derived from fully human sequences, do not require humanization for e.g. therapeutical use in humans. As in the case of VHH domains, they are well expressed also in prokaryotic expression systems, providing a significant reduction in overall manufacturing cost.
  • Affinity-matured immunoglobulin single variable domain molecules of the invention may be prepared by methods known in the art, for example, as described by Marks et al., 1 992, Biotechnology 1 0:779-783, or Barbas, et al., 1994, Proc. Nat. Acad.
  • epitopes refer to the part of a macromolecule, such as a polypeptide, that is recognized by antigen-binding molecules, such as conventional antibodies or the polypeptides of the invention, and more particularly by the antigen-binding site of said molecules.
  • Epitopes define the minimum binding site for an immunoglobulin, and thus represent the target of specificity of an
  • biparatopic antigen-binding molecule
  • biparatopic antigen-binding molecule or "biparatopic” polypeptide as used herein shall mean a polypeptide comprising a first immunoglobulin single variable domain and a second immunoglobulin single variable domain as herein defined, wherein these two variable domains are capable of binding to two different epitopes of one antigen, which epitopes are not normally bound at the same time by one monospecific immunoglobulin, such as e.g. a conventional antibody or one immunoglobulin single variable domain.
  • Biparatopic polypeptides can be composed of variable domains which have different epitope specificities, and do not contain mutually complementary variable domain pairs which bind to the same epitope. The two variable domains do therefore not compete with each other for binding to the target.
  • a polypeptide such as an immunoglobulin, an antibody, an immunoglobulin single variable domain, a polypeptide of the invention, or generally an antigen binding molecule or a fragment thereof
  • a polypeptide that can "bind to” or “specifically bind to”, that "has affinity fo and/or that "has specificity for" a certain epitope, antigen or protein (or for at least one part, fragment or epitope thereof) is said to be
  • the term “specificity” refers to the number of different types of antigens or epitopes to which a particular antigen-binding molecule or antigen- binding protein (such as an immunoglobulin, an antibody, an immunoglobulin single variable domain, or a polypeptide of the invention) can bind.
  • the specificity of an antigen-binding protein can be determined based on its affinity and/or avidity.
  • the affinity represented by the equilibrium constant for the dissociation of an antigen with an antigen-binding protein (KD) is a measure for the binding strength between an epitope and an antigen-binding site on the antigen-binding protein: the lesser the value of the KD, the stronger the binding strength between an epitope and the antigen-binding molecule (alternatively, the affinity can also be expressed as the affinity constant (KA), which is 1/KD).
  • affinity can be determined in a manner known per se, depending on the specific antigen of interest.
  • Avidity is the measure of the strength of binding between an antigen- binding molecule (such as an immunoglobulin, an antibody, an immunoglobulin single variable domain, or a polypeptide of the invention) and the pertinent antigen. Avidity is related to both the affinity between an epitope and its antigen binding site on the antigen-binding molecule and the number of pertinent binding sites present on the antigen-binding molecule.
  • an antigen- binding molecule such as an immunoglobulin, an antibody, an immunoglobulin single variable domain, or a polypeptide of the invention
  • Avidity is related to both the affinity between an epitope and its antigen binding site on the antigen-binding molecule and the number of pertinent binding sites present on the antigen-binding molecule.
  • Amino acid residues will be indicated according to the standard three-letter or one-letter amino acid code, as generally known and agreed upon in the art.
  • amino acid difference refers to insertions, deletions or substitutions of the indicated number of amino acid residues at a position of the reference sequence, compared to a second sequence.
  • substitution(s) will preferably be conservative amino acid substitution(s), which means that an amino acid residue is replaced with another amino acid residue of similar chemical structure and which has little or essentially no influence on the function, activity or other biological properties of the polypeptide.
  • conservative amino acid substitutions are well known in the art, for example from WO 98/491 85, wherein conservative amino acid substitutions preferably are substitutions in which one amino acid within the following groups (i) - (v) is substituted by another amino acid residue within the same group: (i) small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro and Gly; (ii) polar, negatively charged residues and their (uncharged) amides: Asp, Asn, Glu and Gin; (iii) polar, positively charged residues: His, Arg and Lys; (iv) large aliphatic, nonpolar residues: Met, Leu, lie,
  • a nucleic acid or polypeptide molecule is considered to be "(in) essentially isolated (form)" - for example, when compared to its native biological source and/or the reaction medium or cultivation medium from which it has been obtained - when it has been separated from at least one other component with which it is usually associated in said source or medium, such as another nucleic acid, another protein/polypeptide, another biological component or
  • nucleic acid or polypeptide molecule is considered “essentially isolated” when it has been purified at least 2-fold, in particular at least 10- fold, more in particular at least 100-fold, and up to 1000-fold or more.
  • a nucleic acid or polypeptide molecule that is "in essentially isolated form” is preferably essentially homogeneous, as determined using a suitable technique, such as a suitable chromatographical technique, such as polyacrylamide-gelelectrophoresis; n)
  • sequence identity between e.g. two immunoglobulin single variable domain sequences indicates the percentage of amino acids that are identical between these two sequences. It may be calculated or determined as described in paragraph f) on pages 49 and 50 of WO08/020079. "Sequence similarity" indicates the percentage of amino acids that either are identical or that represent conservative amino acid substitutions.
  • polypeptides of the invention have specificity for human CX3CR1 .
  • the polypeptides of the invention preferably bind to human CX3CR1 (SEQ ID NO: 255).
  • polypeptides of the present invention also bind to cynomolgus CX3CR1 (SEQ ID NO: 256).
  • the invention provides novel pharmaceutically active agents for the prevention, treatment, alleviation and/or diagnosis of CX3CR1 associated diseases, disorders or conditions, such as cardiovascular diseases.
  • the invention provides polypeptides which bind to human CX3CR1 and are capable of blocking the binding of human fractalkine to human CX3CR1 .
  • the polypeptide is an immunoglobulin comprising an antigen-binding domain comprising three complementarity determining regions CDR1 , CDR2 and CDR3, wherein said immunoglobulin binds to human CX3CR1 and is capable of blocking the binding of human fractalkine to human CX3CR1 .
  • the polypeptide comprises one or more anti-CX3CR1 immunoglobulin single variable domain, wherein said polypeptide is capable of blocking the binding of human fractalkine to human CX3CR1 .
  • polypeptide of the present invention is characterized by one or more of the following properties:
  • Bind with high affinity to human CX3CR1 for example at an EC 50 of less than or equal to 10nM, less than or equal to 5nM, less than or equal to 2.5nM or less than or equal to 1 nM, as determined by cell binding FACS;
  • Inhibit fractalkine induced chemotaxis mediated by human CX3CR1 for example at an IC 5 o of less than or equal to 500 nM, or less than or equal to 100 nM, or of less than or equal to 75 nM, or less than or equal to 50 nM, or less than or equal to 10 nM or less than or equal to 5nM; the obtained efficacy of inhibition is more than or equal to 15%, or more than or equal to 50%, or more than or equal to 80%, or more than or equal to 95%; • Inhibit fractalkine induced internalization mediated by human CX3CR1 , for example at an IC 5 o of less than or equal to 10 nM or less than or equal to 5nM;
  • a polypeptide of the present invention further comprises a half-life extending moiety, for example an albumin binding moiety, a polyethylene glycol molecule or a Fc domain.
  • a polypeptide of the present invention comprises two or more anti-CX3CR1 immunoglobulin single variable domains.
  • the two anti-CX3CR1 immunoglobulin single variable domains are covalently linked by a linker peptide.
  • the two anti- CX3CR1 immunoglobulin single variable domains in a polypeptide of the present invention have the same amino acid sequence.
  • the two anti- CX3CR1 immunoglobulin single variable domains in a polypeptide of the present invention have different amino acid sequences.
  • a polypeptide of the present invention comprises two anti-CX3CR1 immunoglobulin single variable domains and further comprises a half-life extending moiety, for example an albumin binding moiety, a polyethylene glycol molecule or a Fc domain.
  • a polypeptide of the present invention comprises a first anti- CX3CR1 immunoglobulin single variable domain covalently linked to an albumin binding moiety by a first linker peptide, wherein said albumin binding moiety is further covalently linked to a second anti-CX3CR1 immunoglobulin single variable domain by a second linker peptide.
  • a polypeptide of the present invention comprises an anti-CX3CR1 immunoglobulin single variable domain covalently linked to a Fc domain by a linker peptide.
  • such polypeptide comprising an anti-CX3CR1 immunoglobulin single variable domain covalently linked to a Fc domain by a linker peptide is provided as a dimer, for example through disulfide bridges.
  • Single variable domains of the present invention were identified from a library expressing single variable domains (VHH) derived from a llama immunized with DNA encoding human CX3CR1 .
  • the phage library was panned on hCX3CR1 viral lipoparticles and binding phage were screened for their ability to compete for receptor binding with Alexa-fluor labeled fractalkine (AF-FKN).
  • AF-FKN Alexa-fluor labeled fractalkine
  • an immunoglobulin single variable domain of the present invention consists essentially of four framework regions (FR1 , FR2, FR3 and FR4) and three complementary determining regions (CDR1 , CDR2 and CDR3).
  • the immunoglobulin single variable domain has the structure FR1 - CDR1 - FR2 - CDR2 - FR3 - CDR3 - FR4.
  • the immunoglobulin single variable domain is an antibody domain.
  • the CDR3 of a polypeptide of the present invention in particular a immunoglobulin single domain of the present invention has the amino acid sequence of Asp-Xaa1 -Arg-Arg-Gly-Trp-Xaa2-Xaa3-Xaa4-Xaa5 as set forth in SEQ ID NO: 197, wherein:
  • - Xaa1 is Pro, Ala or Gly;
  • - Xaa2 is Asp or Asn
  • - Xaa3 is Thr or Ser
  • - Xaa4 is Arg, Lys, Ala or Gly
  • - Xaa5 is Tyr or Phe.
  • the CDR3 of a polypeptide of the present invention in particular a immunoglobulin single domain of the present invention, has the amino acid sequence of Asp-Xaa1 -Arg-Arg-Gly-Trp-Xaa2-Xaa3-Xaa4-Xaa5 as set forth in SEQ ID NO: 197, wherein:
  • - Xaa1 is Pro, Ala or Gly;
  • - Xaa2 is Asp or Asn
  • - Xaa4 is Arg or Lys
  • the CDR3 of a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the amino acid sequence of Asp-Pro-Arg-Arg-Gly-Trp-Asp-Thr-Arg-Tyr as set forth in SEQ ID NO: 186.
  • a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the following CDR1 , CDR2 and CDR3:
  • a) has the amino acid sequence of GSIFSSNAMA (SEQ ID NO: 141 ); or b) has an amino acid sequence that has at least 80% amino acid identity with the amino acid sequence of SEQ ID NO: 141 ; or
  • c) has an amino acid sequence that has 2, or 1 amino acid(s) difference with the amino acid sequence of SEQ ID NO: 141 , wherein
  • d) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a) has the amino acid sequence of GINSVGITK (SEQ ID NO: 164); or b) has an amino acid sequence that has at least 70% amino acid identity with the amino acid sequence of SEQ ID NO: 164; or
  • c) has an amino acid sequence that has 4, 3, 2, or 1 amino acid(s)
  • d) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a) has the amino acid sequence of DPRRGWDTRY (SEQ ID NO: 186); or b) has an amino acid sequence that has at least 70% amino acid identity the amino acid sequence of SEQ ID NO: 186; or
  • c) has an amino acid sequence that has 3, 2, or 1 amino acid(s) difference with the amino acid sequences of SEQ ID NO: 186, wherein
  • d) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a polypeptide of the present invention in particular a immunoglobuling single domain of the present invention, has the following CDR1 , CDR2 and CDR3, wherein:
  • said CDR1 has the amino acid sequence of GRTFSSYAMG (SEQ ID NO:
  • said CDR2 has an amino acid sequence that a) has at least 90% amino acid identity with the amino acid sequence of GISGSASRKY (SEQ ID NO: 176) or b) has the amino acid sequence of SEQ ID NO: 176 or 177; and said CDR3 has the amino acid sequence of SNSYPKVQFDY (SEQ ID NO:
  • a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the following CDR1 , CDR2 and CDR3:
  • a) has the amino acid sequence of GTIFSNNAMG (SEQ ID NO: 147); or b) has an amino acid sequence that has 6, 5, 4, 3, 2, or 1 amino acid(s) difference with the amino acid sequence of SEQ ID NO: 147, wherein
  • c) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a) has the amino acid sequence of SISNSGSTN (SEQ ID NO: 179); or b) has an amino acid sequences that has 4, 3, 2, or 1 amino acid(s) difference with the amino acid sequence of SEQ ID NO: 179, wherein
  • c) has an amino acid sequence selected from any one of SEQ ID NO's:
  • a) has the amino acid sequence of DARRGWNTAY (SEQ ID NO: 192); or b) has an amino acid sequence that has at least 80% amino acid identity with the amino acid sequence of SEQ ID NO: 192; or
  • c) has an amino acid sequence that has 2, or 1 amino acid(s) difference with the amino acid sequence of SEQ ID NO: 192, wherein
  • a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the following CDR1 , CDR2 and CDR3:
  • a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the following CDR1 , CDR2 and CDR3:
  • a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the following CDR1 , CDR2 and CDR3:
  • a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the CDR1 , CDR2 and CDR3 set forth in:
  • a polypeptide of the present invention in particular an immunoglobuling single domain of the present invention, has the CDR1 , CDR2 and CDR3 set forth in:
  • polypeptides of the present invention having the CDRs described above are shown in Tables 1 , 2, 3 (representative polypeptides of families 101 , 9 and 1 3, respectively) and 4 (representative polypeptides of optimized variants of family 101 .
  • the present invention provides polypeptides having one or more VHH domains.
  • a VHH domain of the present invention comprises or essentially consists of the sequence set forth in:
  • amino acid sequences that have at least 90% amino acid identity with the amino acid sequences of SEQ ID NO: 3; or
  • amino acid sequences that have 1 1 , 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid difference with the amino acid sequences of SEQ ID NO: 3 or d) an amino acid sequence of any one of SEQ ID NO: 1 -48, or SEQ ID NO:
  • VHH domain of the present invention comprises or essentially consists of the sequence set forth in:
  • VHH domain of the present invention comprises or essentially consists of the sequence set forth in:
  • amino acid sequence that has at least 90% amino acid identity with the amino acid sequences of SEQ ID NO: 67; or c) an amino acid sequence that has 12, 1 1 , 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid difference with the amino acid sequences of SEQ ID NO: 67; or
  • a VHH domain of the present invention comprises or essentially consists of the amino acid sequence set forth in any one of SEQ ID NO: 121 -140, or SEQ ID NO: 222-224.
  • a VHH domain of the present invention comprises or essentially consists of the amino acid sequence set forth in any one of SEQ ID NO: 138-140.
  • a VHH domain of the present invention comprises or essentially consists of the amino acid sequence set forth in any one of SEQ ID NO: 222-224.
  • VHH domains of the present invention are shown in Table 5 and representative optimized VHH domains of the present invention are shown in Table 6 below:
  • SEQ ID NO: 1 -48 are VHH domains of family 101 .
  • SEQ ID NO: 49-52 are VHH domains of family 9.
  • SEQ ID NO: 53-120 are VHH domains of family 13.
  • a polypeptide according to the present invention in particular an immunoglobulin single variable domain of the present invention, is humanized and/or optimized for stability, potency, manufacturability and/or similarity to human framework regions.
  • the polypeptide is humanized and/or sequence optimized in one or more of the following positions (according to Kabat numbering): 1 , 1 1 , 14, 16, 74, 83, 108.
  • the polypeptide comprises one or more of the following mutations: E1 D, S1 1 L, A14P, E16G, A74S, K83R, Q108L.
  • one or more framework regions of a polypeptide according to the present invention are humanized and/or sequence optimized.
  • a polypeptide according to the present invention in particular an immunoglobulin single variable domain of the present invention, comprises framework regions (FR) for example as set forth below:
  • FR1 is selected from any one of SEQ ID NO's: 198-204;
  • FR2 is selected from any one of SEQ ID NO's: 205-208;
  • FR3 is selected form any one of SEQ ID NO's: 209-210; and/or iv) FR4 is selected from any one of SEQ ID NO's: 21 1 -212.
  • Human immunoglobulin framework region sequences that can also be used as framework region sequences for the immunoglobulin single variable domains as described above are known in the art. Also known in the art are methods for humanizing framework regions of immunoglobulin single variable domains derived from species other than humans.
  • one or more CDR regions of a polypeptide according to the present invention, in particular an immunoglobulin single variable domain of the present invention is humanized and/or sequence optimized.
  • a polypeptide according to the present invention, in particular an immunoglobulin single variable domain of the present invention is humanized and/or sequence optimized in one or more of the following positions (according to Kabat numbering): 52, 53.
  • a polypeptide according to the present invention in particular an immunoglobulin single variable domain of the present invention, comprises one or more of the following mutations: N52S, S53T.
  • a polypeptide according to the present invention, in particular an immunoglobulin single variable domain of the present invention comprises a CDR2 selected from any one of SEQ ID NO's: 214-221 .
  • Table 7a shows the FR1 -CDR1 -FR2-CRD2 of the sequence optimized variants
  • table 7b shows FR3-CDR3-FR4-CDR4 of said variants.
  • SEQ sequence numbers in the tables
  • Table 7a Sequence optimized variants (FR1 -CDR1 -FR2-CDR2)
  • a polypeptide of the invention can additionally contain modifications such as glycosyl residues, modified amino acid side chains, and the like.
  • polypeptides of the invention are preferably directed against human CX3CR1 , whereas for veterinary purposes, the polypeptides of the invention are preferably directed against CX3CR1 from the species to be treated.
  • the immunoglobulin single variable domains comprised in the polypeptides according to the invention are preferably humanized
  • an immunoglobulin single variable domain can be a domain antibody, i.e. VL or VH antibody, and/or VHH domains as described above, and/or any other sort of immunoglobulin single variable domain, for example camelized VH, provided that these immunoglobulin single variable domains are anti-CX3CR1 immunoglobulin single variable domains.
  • the immunoglobulin single variable domain essentially consists of either a domain antibody sequence or a VHH domain sequence as described above.
  • the immunoglobulin single variable domain essentially consists of a VHH domain sequences.
  • a polypeptide of the present invention comprises two or more anti-CX3CR1 immunoglobulin single variable domains.
  • a polypeptide of the present invention comprises two anti-CX3CR1 immunoglobulin single variable domains, for example anti-CX3CR1 VHHs.
  • the two anti-CX3CR1 immunoglobulin single variable domains in a polypeptide of the present invention have the same amino acid sequence.
  • the two anti-CX3CR1 immunoglobulin single variable domains in a polypeptide of the present invention have different amino acid sequences.
  • immunoglobulin single variable domains present in a polypeptide of the invention can be linked to each other directly (i.e. without use of a linker) or via a linker.
  • the linker is preferably a linker peptide and will, according to the invention, be selected so as to allow binding of the at least two immunoglobulin single variable domains to CX3CR1 , either within one and the same CX3CR1 molecule, or within two different molecules.
  • Suitable linkers will inter alia depend on the epitopes and, specifically, the distance between the epitopes on CX3CR1 to which the immunoglobulin single variable domains bind, and will be clear to the skilled person based on the disclosure herein, optionally after some limited degree of routine experimentation.
  • the two or more anti-CX3CR1 immunoglobulin single variable domains are domain antibodies or VHH domains, they may also be linked to each other via a third domain antibody or VHH domain (in which the two or more immunoglobulin single variable domains may be linked directly to the third domain antibody or VHH domain or via suitable linkers).
  • a third domain antibody or VHH domain may for example be a domain antibody or VHH domain that provides for an increased half-life, as further described herein.
  • the latter domain antibody or VHH domain may be a domain antibody or VHH domain that is capable of binding to a (human) serum protein such as (human) serum albumin or (human) transferrin, as further described herein.
  • the two or more anti-CX3CR1 immunoglobulin single variable domains may be linked in series (either directly or via a suitable linker) and the third (single) domain antibody or VHH domain (which may provide for increased half-life, as decribed above) may be connected directly or via a linker to one of these two or more aforementioned immunoglobulin sequences.
  • Suitable linkers are described herein in connection with specific polypeptides of the invention and may - for example and without limitation - comprise an amino acid sequence, which amino acid sequence preferably has a length of 5 or more amino acids, 7 or more amino acids, 9 or more amino acids, 1 1 or more amino acids, 15 or more amino acids or at least 1 7 amino acids, such as about 20 to 40 amino acids.
  • the upper limit is not critical but is chosen for reasons of convenience regarding e.g. biopharmaceutical production of such polypeptides.
  • the linker sequence may be a naturally occurring sequence or a non-naturally occurring sequence. If used for therapeutical purposes, the linker is preferably non-immunogenic in the subject to which the polypeptide of the invention is administered.
  • One useful group of linker sequences are linkers derived from the hinge region of heavy chain antibodies as described in WO 96/34103 and WO 94/04678.
  • poly-alanine linker sequences such as Ala-Ala-Ala.
  • linker sequences are Gly/Ser linkers of different length such as (gly x ser y ) z linkers, including (gly ser) 3 , (gly ser) , (gly ser), (gly 3 ser), gly 3 , and (gly 3 ser 2 ) 3 .
  • the linker sequence preferably includes an amino acid residue, such as a cysteine or a lysine, allowing such modification, e.g. PEGylation, in the linker region.
  • a polymer for example a polyethylene glycol (PEG) moiety
  • the linker sequence preferably includes an amino acid residue, such as a cysteine or a lysine, allowing such modification, e.g. PEGylation, in the linker region.
  • linkers are:
  • GGGGS (5 GS linker, SEQ ID NO: 233)

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AU2015322141B2 (en) * 2014-09-26 2018-12-20 Closed Joint Stock Company "Biocad" High affinity and aggregatively stable antibodies on the basis of variable domains Vl and a derivative VHH
US11384151B2 (en) 2012-02-27 2022-07-12 Ablynx N.V. CX3CR1-binding polypeptides comprising immunoglobulin single variable domains
US11406710B2 (en) 2017-09-08 2022-08-09 Takeda Pharmaceutical Company Limited Constrained conditionally activated binding proteins
US11685780B2 (en) 2019-03-05 2023-06-27 Takeda Pharmaceutical Company Limited Single domain antigen binding domains that bind human Trop2
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